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Detection of Alu Exonization Events in Human Frontal Cortex From RNA-Seq Data

Alu exonization events functionally diversify the transcriptome, creating alternative mRNA isoforms and accounting for an estimated 5% of the alternatively spliced (skipped) exons in the human genome. We developed computational methods, implemented into a software called Alubaster, for detecting inc...

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Autores principales: Florea, Liliana, Payer, Lindsay, Antonescu, Corina, Yang, Guangyu, Burns, Kathleen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8460874/
https://www.ncbi.nlm.nih.gov/pubmed/34568430
http://dx.doi.org/10.3389/fmolb.2021.727537
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author Florea, Liliana
Payer, Lindsay
Antonescu, Corina
Yang, Guangyu
Burns, Kathleen
author_facet Florea, Liliana
Payer, Lindsay
Antonescu, Corina
Yang, Guangyu
Burns, Kathleen
author_sort Florea, Liliana
collection PubMed
description Alu exonization events functionally diversify the transcriptome, creating alternative mRNA isoforms and accounting for an estimated 5% of the alternatively spliced (skipped) exons in the human genome. We developed computational methods, implemented into a software called Alubaster, for detecting incorporation of Alu sequences in mRNA transcripts from large scale RNA-seq data sets. The approach detects Alu sequences derived from both fixed and polymorphic Alu elements, including Alu insertions missing from the reference genome. We applied our methods to 117 GTEx human frontal cortex samples to build and characterize a collection of Alu-containing mRNAs. In particular, we detected and characterized Alu exonizations occurring at 870 fixed Alu loci, of which 237 were novel, as well as hundreds of putative events involving Alu elements that are polymorphic variants or rare alleles not present in the reference genome. These methods and annotations represent a unique and valuable resource that can be used to understand the characteristics of Alu-containing mRNAs and their tissue-specific expression patterns.
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spelling pubmed-84608742021-09-25 Detection of Alu Exonization Events in Human Frontal Cortex From RNA-Seq Data Florea, Liliana Payer, Lindsay Antonescu, Corina Yang, Guangyu Burns, Kathleen Front Mol Biosci Molecular Biosciences Alu exonization events functionally diversify the transcriptome, creating alternative mRNA isoforms and accounting for an estimated 5% of the alternatively spliced (skipped) exons in the human genome. We developed computational methods, implemented into a software called Alubaster, for detecting incorporation of Alu sequences in mRNA transcripts from large scale RNA-seq data sets. The approach detects Alu sequences derived from both fixed and polymorphic Alu elements, including Alu insertions missing from the reference genome. We applied our methods to 117 GTEx human frontal cortex samples to build and characterize a collection of Alu-containing mRNAs. In particular, we detected and characterized Alu exonizations occurring at 870 fixed Alu loci, of which 237 were novel, as well as hundreds of putative events involving Alu elements that are polymorphic variants or rare alleles not present in the reference genome. These methods and annotations represent a unique and valuable resource that can be used to understand the characteristics of Alu-containing mRNAs and their tissue-specific expression patterns. Frontiers Media S.A. 2021-09-10 /pmc/articles/PMC8460874/ /pubmed/34568430 http://dx.doi.org/10.3389/fmolb.2021.727537 Text en Copyright © 2021 Florea, Payer, Antonescu, Yang and Burns. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Molecular Biosciences
Florea, Liliana
Payer, Lindsay
Antonescu, Corina
Yang, Guangyu
Burns, Kathleen
Detection of Alu Exonization Events in Human Frontal Cortex From RNA-Seq Data
title Detection of Alu Exonization Events in Human Frontal Cortex From RNA-Seq Data
title_full Detection of Alu Exonization Events in Human Frontal Cortex From RNA-Seq Data
title_fullStr Detection of Alu Exonization Events in Human Frontal Cortex From RNA-Seq Data
title_full_unstemmed Detection of Alu Exonization Events in Human Frontal Cortex From RNA-Seq Data
title_short Detection of Alu Exonization Events in Human Frontal Cortex From RNA-Seq Data
title_sort detection of alu exonization events in human frontal cortex from rna-seq data
topic Molecular Biosciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8460874/
https://www.ncbi.nlm.nih.gov/pubmed/34568430
http://dx.doi.org/10.3389/fmolb.2021.727537
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